Variant report

Variant	rs12723353
Chromosome Location	chr1:216984496-216984497
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11117687	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1126021	0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12568029	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12727957	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12733125	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12742081	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12745662	0.94[CHB][hapmap];0.85[EUR][1000 genomes]
rs12753723	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12760372	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1344874	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1545109	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1545110	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1821787	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1971804	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2164613	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2164614	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6604646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7526618	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7528362	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7531310	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7543938	0.83[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762163	chr1:216982140-217015625	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
2	esv3430243	chr1:216983179-216985177	Enhancers Weak transcription Genic enhancers	TF binding region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12723353	C1orf97	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216979000-216986200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:216979800-216985000	Weak transcription	Fetal Heart	heart
3	chr1:216979800-216985200	Weak transcription	Brain Substantia Nigra	brain
4	chr1:216979800-216988800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:216979800-216989000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:216980000-216984800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:216980200-216986400	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:216980200-216987400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:216980400-216988000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:216981200-216986000	Weak transcription	HSMMtube	muscle
11	chr1:216983200-216988600	Weak transcription	Right Atrium	heart
12	chr1:216983200-216989200	Weak transcription	Gastric	stomach
13	chr1:216983600-216986200	Weak transcription	Psoas Muscle	Psoas
14	chr1:216983600-216986400	Weak transcription	Fetal Lung	lung
15	chr1:216983600-216988600	Weak transcription	Left Ventricle	heart
16	chr1:216983600-216988800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:216983800-216985000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:216984000-216985000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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